Heya,
I'm trying to output cuffdiff data into cummeRbund, but it appears to be having issues with connection to a database (below). Does anyone have any suggestions as to how I can fix this? Thanks!
cuffdata <- readCufflinks('/home/sbica1/tophat/finaltrans/tophat/0125diffout')
Creating database /home/sbica1/tophat/finaltrans/tophat/0125diffout/cuffData.db Reading /home/sbica1/tophat/finaltrans/tophat/0125diffout/genes.fpkmtracking Checking samples table... Populating samples table... Writing genes table Reshaping geneData table Recasting Writing geneData table Reading /home/sbica1/tophat/finaltrans/tophat/0125diffout/gene_exp.diff Error in function (classes, fdef, mtable) : unable to find an inherited method for function "make.db.names", for signature "SQLiteConnection", "integer"
csVolcano(genes(cuff_data),'0',36)
Error in .local(object, x, y, features, ...) : One or more values of 'x' or 'y' are not valid sample names!
did you install RSQLite?
Yup. (taking up 15 characters)
Did you try running it twice in a row? Kinda stupid thing to try, but it actually worked for a problem I was having with cummeRbund.
Hi John St. John- I did, but to no avail.
Also- thanks for your suggestion to altering hits.cpp prior to compilation of cufflinks, it sorted out another issue I had.